The Shadow of the Day
by Mysocksarerockin101
Summary: Cipher, an evil organization that steals Pokémon and turns them into fighting machines, is now in the Kanto Region. Skylar is a 17 year old undercover agent tracking down these sinister master minds. Join her shape shifting Mew, partner in crime, Josh, and his trustworthy Gengar as the four of them set out to save the captive Pokémon and reopen the door to their hearts.


Woo hoo! New story! I thought it would be fun to create two characters and also have the villains we all know and love… well mostly hate… so much! This story takes place in the Kanto Region because well… Kanto is just that awesome. Happy reading!

I don't own Pokémon. I only own Skylar and Josh.

Chapter 1: That Stupid Cotton Candy: Skylar's POV

As I worked my way through the air vent, I finally began to hear voices. A dim light was shining in front of me, glittering through an opening blocked off by metal bars. My boss had barely told me anything when I was assigned this mission. All he told me was to go "spy on these people". Kind of hard to know what to look for when I have nothing to expect... but a mission is a mission. I peeked through the small space and watched the action below.

"Process complete." A male scientist in a lab coat says scribbling something on a pad of paper. He had dark hair, almost a gray color, wrapped up into a ponytail and brought to the front of his head. He wore tinted glasses that were small and pointed and a strange necklace that almost looked like a blue 'V'. "Bring in the next one."

Another female scientist brings in a Primeape, gripping the messy haired fighting type firmly by its wrist. The Pokémon was squirming, obviously trying to get away. It was brought to a machine with a giant glass cylinder. The scientist holding its arm opened the door to the container and shoved the Primeape inside, slamming the door behind it.

"Begin the procedure." The scientist with the tinted glasses commanded.

"As you wish, Ein." The female said, typing something into a keyboard connected to the machine. Suddenly a dark purple, almost black, ray shot down from the top of the cylinder, surrounding the Primeape. It squeezed its eyes shut and cried out in pain, falling onto its knees. I put a hand over my mouth to avoid screaming at the horror I was witnessing. Where's Mew when I need her?

A few moments later the ray disappeared and the Pig Monkey Pokémon rested completely motionless, still on its knees. No… they didn't… they couldn't have. Silence filled the lab room as the two scientists stared at the passed out creature, waiting for something to happen.

The Primeape's eyes shot open and it quickly rose to its feet. The female opened the cylinder and the Primeape flipped out, landing perfectly on both feet. There was something different about it… it looked the same on the outside, but there was a more… evil aura about it now. What did the machine do to it…?

"Take it to Venus and ask her where we should send it." The man so called Ein says. The door to the lab opens and in walks in a lady dressed in a lot of… pink. Bleh.

"Were you talking about me?" The very formally dressed woman asks. "I am beautiful and everything but you're making me blush!" She giggles. She has orange hair curled into ringlets and golden eyes. She wore a pink and white dress, almost like a ball gown, and a huge gold crescent moon extends upward from the back of her dress. Pink silk covers her lips and nose and she… never mind. Lets just say she looked like a walking cotton candy.

Ein rolls his eyes and says, "We were just going to ask you where to send this Primeape."

"Maybe Dakim would like it? He is one to fight after all." She winks. Now it was my turn to roll my eyes.

"Would you mind taking it to him?" Ein asks.

"If I must," Venus scowls. "I was going to go visit my fans but I guess they can wait." She has fans? Well I guess I would go to a show to see a cotton candy sing.

"Thank you. Where is Dakim any way?"

"How should I know? The man runs all over the place. His Entei is his best friend and everything." My eyes widen. They have an Entei? They're stronger than I thought… it's kind of hard not to judge them when they have Miss Bubble Gum Sugar Fairy over there whipping her hair for everyone. "The last I heard from him he was on his way to Fuchsia City to get some Pokémon for us in the Safari Zone."

"Then I guess we are heading to Fuchsia City." Ein scratches his chin. "When are the others getting here?"

"They're on the boat now. They should reach the port in about 5 days." Venus smiles. "I can't wait to see Gorigan! He's so muscular!" She gushes jumping up and down like a little girl. I have nothing to say to that.

"Are they bringing the portable machine?"

"I think so! They would be stupid if they didn't! That's why they're coming here isn't it?" She playfully slaps his shoulder. He glares at her and I hold back a laugh.

"Mew! Mew!" I hear my best friend's voice echo through out the vent. She finally comes into view, floating with a happy grin on her face like she always does. Even though I'm not a fan of pink, I made an exception for Mew, besides she rocked the pink fur anyway! She was the best Pokémon any one could ever have and I felt so blessed to have her on my side. She always wears a thick black cloth across her forehead that makes her look like a ninja. These are only some of the many reasons why I love her so much. She stops beside me, looking at me curiously with big baby blue eyes. "**Mew!**" She exclaims loudly, happy to see me.

"What was that?" Ein asks. Oh no. Mew and I freeze. The Primeape sniffs around and finally looks up at us.

"Prime!" It calls. Ein and Venus look up too and are shocked to see a 17 year old agent and a levitating Mew spying on them in the air vent. Well… wouldn't you be surprised too?

"Intruder!" Ein shouts. "Primeape use Seismic Toss!"

The fighting monkey jumps into the air, ready to attack us.

"Mew, Teleport!" I command grabbing onto her. I close my eyes tightly and when I open them again, instead of being in the secret lab in Viridian City, Mew and I were now in Viridian Forest at our campsite. I sigh of relief and hug her.

"Mew!" She exclaims, proud.

"Oh! You're back." I look up and see my best friend, Josh, smiling down at me. Josh has been an undercover agent and my partner for 3 years now. I first met him when I was 14 and I was chasing a Skitty that had been stolen from a little girl by Team Rocket. He mad managed to grab the Skitty and he gave it back to the girl. I still remember first seeing him, his brown hair falling messily down to his eyebrows and his matching brown eyes that mesmerized me every time I looked into them. When he saw me in my uniform he had asked me what organization I was from and he actually signed up to be my partner.

He was my best friend and we told each other everything. When I was 14 I had the biggest crush on the guy that I'm actually surprised he still talks to me to this day. I was so love struck that I would always stare at him and follow him around… he even caught me wearing one of his old t-shirts that I **may** have stolen from his room… I was like a love sick Growlithe. Over the years my feelings slowly drifted away and instead of Josh being my crush, he was like my older brother, but there's always that small place in your heart for all the people you've ever liked, you know?

He was currently opening a package of Pokémon Food, making Mew float over to him and poke his back several times, causing him to smile.

"Nice to see you too." I say sarcastically. He winks at me and pours the food into two bowls, putting one beside Mew and keeping the other in his hands.

"Gengar!" He calls out to his Pokémon. A cold draft blows in, making me shiver, and I feel something grab me from behind.

"**Ahhhh!**" I scream probably jumping ten feet in the air. Josh starts laughing hysterically, Mew giggling along with him. I growl and look up to see a very amused Gengar grinning down at me. After a minute of acting angry I finally start laughing.

"That was great." Josh grins placing the bowl at Gengar's feet.

"I should've seen that coming when I felt the cold breeze." I giggle embarrassed. Josh puts an arm around my shoulders.

"So what happened back there? You never have Mew use Teleport unless you've been caught."

"Let's start a fire and then I'll explain. You aren't going to like it though."

While Mew and Genger were busy playing, Josh and I sat around the fire on wooden logs, him across from me.

"So I was in the air vent," I began. "I heard voices so I stopped to observe what was going on. There was a scientist by the name of Ein…" Josh's eyes opened wide when I said the name, but I ignored it for now. "…and a woman brought in a Primeape. They put it into a machine and a black ray surrounded it. When they powered it off the Primeape didn't look any different but something changed, you could just feel it… and before everything happened it struggled to get away, but afterwards it stayed by their sides."

"Did it attack you?" Josh asks. I found myself staring at him for a moment. Having an attractive 18 year old for a partner really stunk… well it had its advantages, but it mostly stunk. I found myself losing my focus all the time. He on the other hand, was always so focused on his missions… as I should be. "I know I'm hot and everything but you don't need to stare." He jokes with a smile. My cheeks were already burning from the flames of the fire, so hopefully he didn't catch me blushing. Curse my old obsession with this kid when I was 14.

"I was getting there…" I finally managed to say trying to remember where I left off. "Ein was questioning where to take the Primeape but then walked in a lady who was very fond of pink." My voice became annoyed when I brought up Venus. I couldn't stand the lady, even though I've never spoken to her in my life. I normally wasn't one to judge but… never mind I'm just going to stop talking now.

"Venus?" Josh asks with a raised eyebrow while smirking at me. He knew I hated pink. I look at him confused. Had I said her name? I don't think I did… how did he know her name? It couldn't have been a lucky guess or anything.

"How'd you know that?" I ask.

"I'll explain later, just continue." He encourages.

"Well she walked in and her and Ein began to talk. They brought up someone named Dakim and were saying that he was in Fuchsia City at the Safari Zone getting Pokémon for them. They were going to take the Primeape to him too."

"We need to go to Fuchsia City." He says standing up and walking over to his belongings that were stacked up in a pile. He begins to shove things into bags.

"Wait I'm not done." I say.

"You can tell me the rest on the way there. We need to leave now and save those Pokémon." He says getting angry. Josh really amazed me about how passionate he was about Pokémon. I was surprised when he asked to be my partner and didn't go train to be a Pokémon Ranger or something instead. Whenever it comes to Pokémon in trouble, leave it to Josh to save the day.

"Dakim has an Entei." I blurted out, hoping it would stop him from packing up. It did. His back stiffened and he slowly turned around to face me, kneeling on the ground.

"They… have an Entei?" He asks. I slowly nod and he stares at the ground. "Skylar, we have to stop them. I know you don't understand everything right now but please trust me. We need to go after them."

"I do trust you… and I want to save that Primeape." I smile encouragingly at him. "So let's go." I grab his hand and help him up. He smiles at me, making me grin back. We begin to pack up our supplies into three bags and put out the fire.

"Mew, transform into a Dragonite." I tell her. Instead of my small pink floating friend, now standing before me was a large orange dragon with a black material tied across her forehead of course. Mew's ability to transform into any Pokémon was very useful in many situations. Josh puts Gengar in his Pokéball and shoves the sphere into his pocket. I quickly take my blonde hair out of its ponytail and redo it, tossing it back up. I pull out a string, tying the three bags together and connecting them to Mew… well Dragonite's… black fabric so when we were flying they would stay put.

"You ready?" Josh asks, climbing onto Dragonite's back, one hand around her neck and the other stretched out to me.

"You bet." I say grabbing his hand and climbing behind him. I wrap my arms around his waist and he does the same to Dragonite's neck.

"Fly to Fuchsia City." Josh tells her. She begins to flap her wings and we are soon levitating off of the ground. The trees of Viridian Forest began to get smaller and smaller as we rose higher into the air and shortly disappeared behind the low clouds.

"How did you know about Venus?" I ask Josh. He remains quiet, ignoring my question. I sigh. "Do you know what they did to that Primeape?"

"Yes." He answers short and simple.

"Do you want me to stop asking you questions?" I ask. He laughs.

"Technically you just asked me a question."

"Oh you know what I mean."

He laughs and says, "I don't mind the questions. It's just a touchy subject for me... you know how I am when it comes to people abusing Pokémon, whether its physically or mentally… but you have a right to know." He takes in a breath. "Ein and Venus are from a group named Cipher. They believe in stealing Pokémon and turning them into fighting machines by closing the door to their hearts. Once a Pokémon's heart is closed it becomes filled with anger and will even attack a human if told to. A closed heart is very hard to open back up, but it isn't impossible. Cipher wants to turn all the Pokémon into fighting machines and take over the world."

I watch the clouds as he spoke. It was so hard to imagine that there were people out there that believed doing such evil things was right. All those poor Pokémon being forced to do things they don't want to do. We had to deal with horrible people like this at least 3 times a month, of course we didn't mind because it was our job, but was bothered us was the fact that these people had the dignity to do the things they do.

"So when were you planning on telling me this?" I ask.

"When Boss assigned us the mission he told me to wait to tell you this until you were ready. I figured since you saw the transformation yourself, you were."

"So you and Boss sent me to spy on the lab so I would understand what was going on?"

"Yep." He pops the 'p'.

"How can they do such a thing? How can they think that doing something so stupid and evil is right? It's almost like they are all-"

"I know," Josh cuts me off before I began my rant. Smart boy.

"There's more I need to tell you."

"Spill it."

"They were saying that others were coming here. They were bringing some portable machine with them."

"Did they say what the machine was for?"

"No, that's all they said." I say looking at the back of his head. I guess eye contact really isn't possible when you're riding Dragonite back.

"Did they say when the others would be here?"

"In 5 days. They said they were going to meet them at 'the port'. I'm guessing they're referring to the one in Vermilion City."

"Probably. You should get some rest before we get there. It will be a couple hours anyway."

"Are you sure? Do you want to sleep?"

"While you were gone Genger used Hypnosis on me because I was so tired but refused to sleep incase you needed my help."

I couldn't help but laugh. Genger was such a character.

"Wake me up a few minutes before we get there."

"I will."

We finally reached Fuchsia City, but when we did I immediately wanted to leave. People were running around, going crazy. Screaming citizens piled out of the Safari Zone building. Dragonite lands and we quickly hop off, unloading our belongings.

"Gengar, come on out!" Josh says throwing his Pokéball into the air. Gengar comes out and looks down at its trainer. Yeah… he's a big Gengar.

"Take these bags to the Pokémon Center. Come meet us in the Safari Zone when you're done."

"Gengar!" It says taking the bags and heading towards the red and white building.

"What's going on?" Josh asks as a guy about 13 or 14 runs past.

"Some psycho dude is trying to take all the Pokémon in the Safari Zone! He has an Entei that was going to attack us unless we evacuated!" The boy says before running away from us.

"That's our cue." Josh says. I nod as we charge into the building that everyone was running out of.

(I hope you guys like it! I really appreciate all the positive reviews and comments from everyone. Comment, rate, review! Thanks for reading!)


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